Defining the Host Genetic Control of the Barley Rhizosphere Microbiota

Abstract

Limiting environmentally harmful consequences of crop production while increasing productivity amid climatic modifications is one of the major challenges facing agriculture in the XXIst century. Crucially, over the course of the next 30 years, innovative strategies are required to tackle this challenge and ensure a sustainable and safe access to food resources to a global population of over 9 billion people in 2050.

One of these strategies proposes to exploit the microbial communities thriving in association with plant roots, collectively referred to as the rhizosphere microbiota, to uncouple profitable crop yield from the input of synthetic compounds in the agroecosystem. In the last decade technical advances have allowed scientists to gain unprecedented insights into plant-microbiota interactions in the rhizosphere.

However, a precise understanding of how plants can shape these communities is still missing. This is information will be crucial to assist breeders in developing crops capable of maximising the mutualistic relationships with soil microbes. To fill this knowledge gap, in this thesis I use Barley (Hordeum vulgare), a global crop and an excellent experimental model, and will capitalise on state-of-the art sequencing and computational approaches to gain fundamentally novel insights into the host genetic control of the rhizosphere microbiota.

The overarching hypothesis of my work is that the host genotype has the capacity to shape the rhizosphere microbiota to sustain plant growth in given soil conditions. I further hypothesize that this capacity impacts both the taxonomic and functional compositions of the rhizosphere microbiota and can be ultimately traced to loci in the barley genome. To test these hypotheses, I developed three major experimental lines aimed at a) characterising the microbiota of wild and cultivated barley genotypes grown in agricultural soils and how this impacts on plant growth; b) assessing the modulation of structure and function of the rhizosphere microbiota by the plant host under different nitrogen regimes and c) identifying the barley genetic region(s) responsible for the microbiota recruitment using experimental segregating populations between wild and modern barley genotypes. These experiments will contribute to decipher the genetic relationships between a plant genome and its associated microbiota and, in the long term, they will be key to devise novel strategies to enhance nutrient uptake efficiency in cereals.